anjalijain22
commented
2 years ago - Error message:
- Currently, vcfanno annotates the VCF's with two fields (CLNSIG and CLNREVSTAT) taken directly from the ClinVar VCF and an additional field called "clinvar_sig" which is post annotated and its value depends on the value of CLNSIG.
- In ClinVar VCF files from 2016, the CLNSIG column had a numeric datatype where 0 denoted 'uncertain', 2 denoted 'benign', 5 was 'pathogenic', 255 was 'other' and so on. In this situation, we would use the postannotation block to add an additional column called "clinvar_sig" containing relevant descriptions of the numbers in CLNSIG
- However, in the latest ClinVar VCF files the CLNSIG column contains the pathogenicity status instead of the numbers. Therefore, we no longer require this postannotation block and the additional "clinvar_sig" column